This README file has instructions to run a test for positive selection on candidate genes for cancer resistant species.
ssh <username>@hoffman2.ucla.eduTo get a computing node and run your job interactively type the
following:
qrsh
This will give you a cpu with one gigabyte of memory and one hour. This
should be enough for today’s exercise.
You should get a success login notification like this:
Last login: Fri Jun 27 20:59:39 2025 from
172.16.96.79
Notice that you have switched from a login node to a computer node.You
should see something like this.
[dechavez@n1825 ~]$
Note: you may get a different cpu than
n1815**
Get to the workshop directory.
Lest check your current directory by typing pwd
[dechavez@login4 ~]$ /u/home/d/dechavez
Now, to get into the workshop directory type the following:
cd $SCRATCH/EcoEvoBio-Cancer
If you type pwd you should be located at:
/u/scratch/d/dechavez/EcoEvoBio-Cancer
To create you personal directory, change the following code with
your First name and the first to letters of your last name
mkdir DanielCH
Navigate into your directory. Note: you should type the name of
your directory in the following code cd DanielCH
Alignment of the MYC gene.
./scripts/muscle3.8.31_i86linux64 -in aligned_MYC.fasta -out aligned_MYC.fasta
Note: you wont be able to build a tree unless you aligned it
first
Build maximum likelihood phylogeny.
module load iqtree/2.2.2.6iqtree2 -s aligned_MYC.fastacd modelAnano codeml.ctlcd ../modelAnullnano codeml.ctlcd ../scriptsTo identify your job once is submitted into the
cluster, you need to add your initials to the
name of your job. So let’s replace the job id from
DCHmodelA with your initials. For instance,
Charles Darwin should have CDAmodelA
Add your initials into the script for the positive selection
model.
nano modelA.sh
Now add your initials for the null model scripts.
cd ../modelAnull
nano modelAnull.sh
Then submit the job to run PAML for the positive selection
model.
qsub modelA.sh
Do the same for the null model.
qsub modelAnull.sh
Make sure that your job is running. You can check the status of
your job with myjobs
Open another terminal and clone this repository
git clone <>
Explore your alignment.
Open the program mesquite.
Type OK if the following window appears
pwd you should be located at:cd into the proper directory.grep 'lnL' modelA/out.modelAgrep 'lnL' modelAnull/out.modelAnullmodule load RRscript script/pvalue.R -7590.727272 -7594.131954grep -A 4 'BEB' modelA/out.modelACongratulations you have learned how to evaluate signals of positive selection in the tree of life !!!!